To handle problems of the low encoding efficiency and the high decoding cost in short-length LT code, a novel joint encoding and decoding optimization method is proposed in this paper. Based on the weighted statistical probability value of original information groups, the encoding optimization algorithm targeting at transmitting original information groups uniformly is presented at the transmitter. And a multi-layer decoding algorithm with vary number of layers, which utilizes the the redundancy information in the stopping set is proposed to achieve a tradeoff between the computation complexity and the redundancy cost at the receiver. Simulation results under different conditions demonstrate that the proposed encoding and decoding optimization method could improve the encoding efficiency significantly and could reduce the decoding overhead effectively.